Two systems were compared for medium-strength dairy wastewater treatment. The first comprised a methanogenic Moving Bed Biofilm Reactor (AnMBBR) and an aerobic MBBR (AeMBBR), while the second an AnMBBR and a sequencing batch reactor (SBR) with Chlorella sorokiniana. The AnMBBR, under ambient conditions, achieves biogas production sufficient enough to attain energy autonomy. The produced energy was 0.538 kWh m, whereas the energy consumption 0.025 kWh m. Its coupling with the AeMBBR removed COD, NH-N TKN, and PO-P by 93 ± 4%, 97 ± 3%, 99 ± 1% and 49 ± 15%, respectively, while the use of the SBR as a second step eliminated totally COD but partially the other pollutants. The higher nitrogen removal in the first system was due to nitrification occurring in the AeMBBR. The acclimatization of microalgae to dairy wastewater enhanced their growth. Their protein content was 54.56%, while starch and lipids were 3.39% and 23.1%, respectively.